Identification of the syr-syp box in the promoter regions of genes dedicated to syringomycin and syringopeptin production by Pseudomonas syringae pv. syringae B301D

Journal of Bacteriology

Volumn 188, Issue 1, 2006, Pages 160-168

  Wang, Nian ^a,b   Lu, Shi En ^a,c   Yang, Qingwu ^a   Sze, Sing Hoi ^a   Gross, Dennis C ^a  

^a TEXAS A AND M UNIVERSITY   (United States)

^b UNIVERSITY OF CALIFORNIA   (United States)

^c MISSISSIPPI STATE UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BETA GLUCURONIDASE; PEPTIDE SYNTHASE; PLANT TOXIN; SYRINGOMYCIN; SYRINGOPEPTIN; UNCLASSIFIED DRUG; BACTERIAL PROTEIN; CYCLOPEPTIDE; LIPOPROTEIN; SYRINGOPEPTIN 22;

ANIMAL CELL; ARTICLE; CISTRON; GENE DELETION; GENE IDENTIFICATION; GENOME ANALYSIS; NONHUMAN; OPERON; PEPTIDE SYNTHESIS; POLYMERASE CHAIN REACTION; PRIORITY JOURNAL; PROMOTER REGION; PSEUDOMONAS SYRINGAE; REPORTER GENE; SEQUENCE ANALYSIS; SITE DIRECTED MUTAGENESIS; BIOSYNTHESIS; CHEMISTRY; GENE EXPRESSION REGULATION; GENETIC TRANSCRIPTION; GENETICS; GENOMIC ISLAND; METABOLISM; MOLECULAR GENETICS; NUCLEOTIDE SEQUENCE;

ANIMALIA; PSEUDOMONAS SYRINGAE; PSEUDOMONAS SYRINGAE PV. SYRINGAE;

BACTERIAL PROTEINS; BASE SEQUENCE; GENE EXPRESSION REGULATION, BACTERIAL; GENOMIC ISLANDS; LIPOPROTEINS; MOLECULAR SEQUENCE DATA; OPERON; PEPTIDES, CYCLIC; PROMOTER REGIONS (GENETICS); PSEUDOMONAS SYRINGAE; TRANSCRIPTION, GENETIC;

EID: 33144484253     PISSN: 00219193     EISSN: None     Source Type: Journal    
DOI: 10.1128/JB.188.1.160-168.2006     Document Type: Article

References (58)

1. Alexeyev, M. F., I. N. Shokolenko, and T. P. Croughan. 1995. Improved antibiotic-resistance gene cassettes and omega elements for Escherichia coli vector construction and in vitro deletion/insertion mutagenesis. Gene 160:63-67.
2. Altschul, S. F., W. Gish, W. Miller, E. W. Myers, and D. J. Lipman. 1990. Basic local alignment search tool. J. Mol. Biol. 215:403-410.
3. Amrein, H., S. Makart, J. Granado, R. Shakya, J. Schneider-Pokorny, and R. Dudler. 2004. Functional analysis of genes involved in the synthesis of syringolin A by Pseudomonas syringae pv. syringae B301D-R. Mol. Plant-Microbe Interact. 17:90-97.
4. Bender, C. L., Alarcón-Chaidez, and D. C. Gross. 1999. Pseudomonas syringae phytotoxins: mode of action, regulation, and biosynthesis by peptide and polyketide synthetases. Microbiol. Mol. Biol. Rev. 63:266-292.
5. Browning, D. F., and S. J. W. Busby. 2004. The regulation of bacterial transcription initiation. Nat. Rev. Microbiol. 2:57-65.
6. N) transcription factor. J. Bacteriol. 182:4129-4136.
7. Chain, P. S. G., E. Carniel, F. W. Larimer, J. Lamerdin, P. O. Stoutland, W. M. Regala, A. M. Georgescu, L. M. Vergez, M. L. Land, V. L. Motin, R. R. Brubaker, J. Fowler, J. Hinnebusch, M. Marceau, C. Medigue, M. Simonet, V. Chenal-Francisque, B. Souza, D. Dacheux, J. M. Elliott, A. Derbise, L. J. Hauser, and E. Garcia. 2004. Insights into the evolution of Yersinia pestis through whole-genome comparison with Yersinia pseudotuberculosis. Proc. Natl. Acad. Sci. USA 101:13826-13831.
8. Choi, S. H., and E. P. Greenberg. 1992. Genetic dissection of DNA-binding and luminescence gene activation by the Vibrio fischeri LuxR protein. J. Bacteriol. 174:4064-4069.
9. pss, the fluorescent siderophore produced by Pseudomonas syringae pv. syringae. J. Bacteriol. 169:2207-2214.
10. Collado-Vides, J., G. Moreno-Hagelsieb, and A. Medrano-Soto. 2002. Microbial computational genomics of gene regulation. Pure Appl. Chem. 74:899-905.
11. Dunlap, P. V., and E. P. Greenberg. 1988. Control of Vibrio fischeri lux gene transcription by a cyclic AMP receptor protein-LuxR protein regulatory circuit. J. Bacteriol. 170:4040-4046.
12. Egland, K. A., and E. P. Greenberg. 1999. Quorum sensing in Vibrio fischeri: elements of the luxI promoter. Mol. Microbiol. 31:1197-1204.
13. Ermolaeva, M. D., O. White, and S. L. Salzberg. 2001. Prediction of operons in microbial genomes. Nucleic Acids Res. 29:1216-1221.
14. Farnham, P. J., and T. Platt. 1981. Rho-independent termination: dyad symmetry in DNA causes RNA polymerase to pause during transcription in vitro. Nucleic Acids Res. 9:563-577.
15. Fernández de Henestrosa, A. R., T. Ogi, S. Aoyagi, D. Chafin, J. J. Hayes, H. Ohmori, and R. Woodgate. 2000. Identification of additional genes belonging to the LexA regulon in Escherichia coli. Mol. Microbiol. 35:1560-1572.
16. Fouts, D. E., R. B. Abramovitch, J. R. Alfano, A. M. Baldo, C. R. Buell, S. Cartinhour, A. K. Chatterjee, M. D'Ascenzo, M. L. Gwinn, S. G. Lazarowitz, N. C. Lin, G. B. Martin, A. H. Rehm, D. J. Schneider, K. van Dijk, X. Y. Tang, and A. Collmer. 2002. Genomewide identification of Pseudomonas syringae pv. tomato DC3000 promoters controlled by the HrpL alternative sigma factor. Proc. Natl. Acad. Sci. USA 99:2275-2280.
17. Grant, S. G. N., J. Jessee, F. R. Bloom, and D. Hanahan. 1990. Differential plasmid rescue from transgenic mouse DNAs into Escherichia coli methylation-restriction mutants. Proc. Natl. Acad. Sci. USA 87:4645-4649.
18. Gross, D. C. 1991. Molecular and genetic analysis of toxin production by pathovars of Pseudomonas syringae. Annu. Rev. Phytopathol. 29:247-278.
19. Gruber, T. M., and C. A. Gross. 2003. Multiple sigma subunits and the partitioning of bacterial transcription space. Annu. Rev. Microbiol. 57:441-466.
20. Feil, H., W. S. Feil, P. Chain, F. Larimer, G. DiBartolo, A. Copeland, A. Lykidis, S. Trong, M. Nolan, E. Goltsman, J. Thiel, S. Malfatti, J. E. Loper, A. Lapidus, J. C. Detter, M. Land, P. M. Richardson, N. C. Kyrpides, N. Ivanova, and S. E. Lindow. 2005. Comparison of the complete genome sequences of Pseudomonas syringae pv. syringae B728a and pv. tomato DC3000. Proc. Natl. Acad. Sci. USA 102:11064-11069.
21. S (RpoS) subunit of RNA polymerase. Microbiol. Mol. Biol. Rev. 66:373-395.
22. Huerta, A. M., H. Salgado, D. Thieffry, and J. Collado-Vides. 1998. RegulonDB: a database on transcriptional regulation in Escherichia coli. Nucleic Acids Res. 26:55-59.
23. Kang, H., and D. C. Gross. 2005. Characterization of a resistance-nodulation-cell division transporter system associated with the syr-syp genomic island of Pseudomonas syringae pv. syringae. Appl. Environ. Microbiol. 71:5056-5065.
24. Kobayashi, N., K. Nishino, and A. Yamaguchi. 2001. Novel macrolide-specific ABC-type efflux transporter in Escherichia coli. J. Bacteriol. 183:5639-5644.
25. Lawrence, J. G. 2003. Gene organization: selection, selfishness, and serendipity. Annu. Rev. Microbiol. 57:419-440.
26. Lazdunski, A. M., I. Ventre, and J. N. Sturgis. 2004. Regulatory circuits and communication in gram-negative bacteria. Nat. Rev. Microbiol. 2:581-592.
27. Lesnik, E. A., R. Sampath, H. B. Levene, T. J. Henderson, J. A. Mcneil, and D. J. Ecker. 2001. Prediction of rho-independent transcriptional terminators in Escherichia coli. Nucleic Acids Res. 29:3583-3594.
28. Loh, J., E. A. Pierson, L. S. Pierson, G. Stacey, and A. Chatterjee. 2002. Quorum sensing in plant-associated bacteria. Curr. Opin. Plant Biol. 5:285-290.
29. Lu, S. E., B. K. Scholz-Schroeder, and D. C. Gross. 2002. Characterization of the salA, syrF, and syrG regulatory genes located at the right border of the syringomycin gene cluster of Pseudomonas syringae pv. syringae. Mol. Plant-Microbe Interact. 15:43-53.
30. Lu, S. E., N. Wang, J. L. Wang, Z. J. Chen, and D. C. Gross. 2005. Oligonucleotide microarray analysis of the salA regulon controlling phytotoxin production by Pseudomonas syringae pv. syringae. Mol. Plant-Microbe Interact. 18:324-333.
31. McGuire, A. M., J. D. Hughes, and G. M. Church. 2000. Conservation of DNA regulatory motifs and discovery of new motifs in microbial genomes. Genome Res. 10:744-757.
32. Mo, Y. Y., and D. C. Gross. 1991. Expression in vitro and during plant pathogenesis of the syrB gene required for syringomycin production by Pseudomonas syringae pv. syringae. Mol. Plant-Microbe Interact. 4:28-36.
33. Navarre, W. W., T. A. Halsey, D. Walthers, J. Frye, M. McClelland, J. L. Potter, L. J. Kenney, J. S. Gunn, F. C. Fang, and S. J. Libby. 2005. Co-regulation of Salmonella enterica genes required for virulence and resistance to antimicrobial peptides by SlyA and PhoP/PhoQ. Mol. Microbiol. 56:492-508.
34. Notredame, C., D. G. Higgins, and J. Heringa. 2000. T-Coffee: a novel method for fast and accurate multiple sequence alignment. J. Mol. Biol. 302:205-217.
35. 34a. Olsen, R. H., G. DeBusscher, and W. R. McCombie. 1982. Development of broad-host-range vectors and gene banks: self-cloning of the Pseudomonas aeruginosa PAO chromosome. J. Bacteriol. 150:60-69.
36. 70 family of sigma factors. Genome Biol. 4:203.
37. Paulsen, I. T., C. M. Press, J. Ravel, D. Y. Kobayashi, G. S. A. Myers, D. V. Mavrodi, R. T. Deboy, R. Seshadri, Q. H. Ren, R. Madupu, R. J. Dodson, A. S. Durkin, L. M. Brinkac, S. C. Daugherty, S. A. Sullivan, M. J. Rosovitz, M. L. Gwinn, L. W. Zhou, D. J. Schneider, S. W. Cartinhour, W. C. Nelson, J. Weidman, K. Watkins, K. Tran, H. Khouri, E. A. Pierson, L. S. Pierson, L. S. Thomashow, and J. E. Loper. 2005. Complete genome sequence of the plant commensal Pseudomonas fluorescens Pf-5. Nat. Biotechnol. 23:873-878.
38. Peñaloza-Vázquez, A., and C. L. Bender. 1998. Characterization of CorR, a transcriptional activator which is required for biosynthesis of the phytotoxin coronatine. J. Bacteriol. 180:6252-6259.
39. Quigley, N. B., and D. C. Gross. 1994. Syringomycin production among strains of Pseudomonas syringae pv. syringae: conservation of the syrB and syrD genes and activation of phytotoxin production by plant signal molecules. Mol. Plant-Microbe Interact. 7:78-90.
40. Quigley, N. B., Y. Y. Mo, and D. C. Gross. 1993. SyrD is required for syringomycin production by Pseudomonas syringae pathovar syringae and is related to a family of ATP-binding secretion proteins. Mol. Microbiol. 9:787-801.
41. Salanoubat, M., S. Genin, F. Artiguenave, J. Gouzy, S. Mangenot, M. Arlat, A. Billault, P. Brottier, J. C. Camus, L. Cattolico, M. Chandler, N. Choisne, C. Claudel-Renard, S. Cunnac, N. Demange, C. Gaspin, M. Lavie, A. Moisan, C. Robert, W. Saurin, T. Schiex, P. Siguier, P. Thébault, M. Whalen, P. Wincker, M. Levy, J. Weissenbach, and C. A. Boucher. 2002. Genome sequence of the plant pathogen Ralstonia solanaceatum. Nature 415:497-502.
42. Sambrook, J., E. F. Fritsch, and T. Maniatis. 1989. Molecular cloning: a laboratory manual. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y.
43. Schnider, U., C. Keel, C. Blumer, J. Troxler, G. Défago, and D. Haas. 1995. Amplification of the housekeeping sigma factor in Pseudomonas fluorescens CHA0 enhances antibiotic production and improves biocontrol abilities. J. Bacteriol. 177:5387-5392.
44. Scholz-Schroeder, B. K., M. L. Hutchison, I. Grgurina, and D. C. Gross. 2001. The contribution of syringopeptin and syringomycin to virulence of Pseudomonas syringae pv. syringae strain B301D on the basis of sypA and syrB1 biosynthesis mutant analysis. Mol. Plant-Microbe Interact. 14:336-348.
45. Scholz-Schroeder, B. K., J. D. Soule, and D. C. Gross. 2003. The sypA, sypB and sypC synthetase genes encode twenty-two modules involved in the non-ribosomal peptide synthesis of syringopeptin by Pseudomonas syringae pv. syringae B301D. Mol. Plant-Microbe Interact. 16:271-280.
46. Schweizer, H. D. 1993. Small broad-host-range gentamycin resistance gene cassettes for site-specific insertion and deletion mutagenesis. BioTechniques 15:831-834.
47. Stevens, A. M., N. Fujita, A. Ishihama, and E. P. Greenberg. 1999. Involvement of the RNA polymerase α-subunit C-terminal domain in LuxR-dependent activation of the Vibrio fischeri luminescence genes. J. Bacteriol. 181:4704-4707.
48. Streips, U. N., and R. E. Yasbin. 2002. Modern microbial genetics. Wiley-Liss, Inc., New York, N.Y.
49. Tartof, K. D., and C. A. Hobbs. 1988. New cloning vectors and techniques for easy and rapid restriction mapping. Gene 67:169-182.
50. Teichmann, S. A., and M. M. Babu. 2002. Conservation of gene co-regulation in prokaryotes and eukaryotes. Trends Biotechnol. 20:407-410.
51. 2-dependent halogenase. Proc. Natl. Acad. Sci. USA 102:10111-10116.
52. Vidaver, A. K. 1967. Synthetic and complex media for rapid detection of fluorescence of phytopathogenic pseudomonads: effect of carbon source. Appl. Microbiol. 15:1523-1524.
53. Wagner, V. E., D. Bushnell, L. Passador, A. I. Brooks, and B. H. Iglewski. 2003. Microarray analysis of Pseudomonas aeruginosa quorum-sensing regulons: effects of growth phase and environment. J. Bacteriol. 185:2080-2095.
54. Wang, L., C. L. Bender, and M. S. Ullrich. 1999. The transcriptional activator CorR is involved in biosynthesis of the phytotoxin coronatine and binds to the cmaABT promoter region in a temperature-dependent manner. Mol. Gen. Genet. 262:250-260.
55. Wang, N., S.-E. Lu, J. Wang, Z. J. Chen, and D. C. Gross. The expression of genes encoding lipodepsipeptide phytotoxins by Pseudomonas syringae pv. syringae is coordinated in response to plant signal molecules. Mol. Plant-Microbe Interact., in press.
56. West, S. E. H., H. P. Schweizer, C. Dall, A. K. Sample, and L. J. Runyenjanecky. 1994. Construction of improved Escherichia-Pseudomonas shuttle vectors derived from pUC18/19 and sequence of the region required for their replication in Pseudomonas aeruginosa. Gene 148:81-86.
57. Yoshida, K., H. Yamaguchi, M. Kinehara, Y. Ohki, Y. Nakaura, and Y. Fujita. 2003. Identification of additional TnrA-regulated genes of Bacillus subtilis associated with a TnrA box. Mol. Microbiol. 49:157-165.
58. Zhang, J. H., N. B. Quigley, and D. C. Gross. 1995. Analysis of the syrB and syrC genes of Pseudomonas syringae pv. syringae indicates that syringomycin is synthesized by a thiotemplate mechanism. J. Bacteriol. 177:4009-4020.